June 2008 Volume 5 Number 6, pp 457 - 575
Visit Nature Methods online to browse the journal.
Now available at http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80ezz0E5
Please note that you need to be a subscriber to enjoy full text access to Nature Methods online. To purchase a subscription, please visit:
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80dtT0EL
Alternatively, to recommend a subscription to your library, please visit
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BRQi0Et
=====================================================================
AmpliTaq Gold(R) Fast PCR Master Mix, UP
The new AmpliTaq Gold(R) Fast PCR Master Mix, UP is optimized for use
in sequencing applications. It provides specific, high-yield amplicons
that can be sequenced easily and robustly. This premixed master mix w
orks with your existing primers to provide sensitive, specific and
reproducible results. Learn more:
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwIW0E5
=====================================================================
=====================================================================
The Source Event – London, 26/09/2008
Now in its 2nd successful year, The Source Event is a dedicated science
career fair from Naturejobs, combining a dynamic exhibition with
conference and workshop sessions. The programme is divided into 3
streams: Graduate, Post Doc and Non-traditional careers. Exhibitors
include a wide range of employers, recruitment agencies and governmental
institutions.
Register now at: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwBw0EV
=====================================================================
=====================================================================
FREE TRIAL AVAILABLE:
SciBX: Science-Business eXchange
To keep up with emerging business-critical science you can read the top 40 journals - or you can read the weekly SciBX analysis. The SciBX team evaluates over 400 papers each week and distills the must-read science.
To find out which papers made it into SciBX this week, sign up for a FREE TRIAL at http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80Burw0EH
=====================================================================
----------------------
EDITORIAL
----------------------
The smaller the better p457
Biologists are increasingly interested in single-molecule approaches. In this issue, a Focus provides a biologist's guide to this relatively new field, and two papers present advances in nanoscale visualization.
doi:10.1038/nmeth0608-457
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwBx0EW
----------------------
CORRESPONDENCE
----------------------
Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry pp459 - 460
Michael L Nielsen et al.
doi:10.1038/nmeth0608-459
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwBy0EX
----------------------
RESEARCH HIGHLIGHTS
----------------------
Tuning in to flower power p463
Researchers generated a high-resolution snapshot of the epigenome of Arabidopsis thaliana by constructing and integrating the methylome, transcriptome and small RNAome using next-generation sequencing.
Michelle Pflumm
doi:10.1038/nmeth0608-463a
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwBz0EY
Mapping the Arabidopsis proteome p463
doi:10.1038/nmeth0608-463b
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwB10EL
Motionless fast 3D scanning pp464 - 465
A 3D laser scanning microscopy method requiring no moving parts promises to expand the in vivo study of fast neuronal signaling at cellular and subcellular levels.
Daniel Evanko
doi:10.1038/nmeth0608-464a
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwB20EM
Rewiring E. coli pp464 - 465
By adding new connections between unrelated genes to a gene network, researchers can investigate network robustness and evolvability.
Allison Doerr
doi:10.1038/nmeth0608-464b
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwB30EN
News in brief p465
doi:10.1038/nmeth0608-465
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwB40EO
A map for fly explorers p466
Virtual composite images generate a map of gene expression in Drosophila embryos.
Natalie de Souza
doi:10.1038/nmeth0608-466
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwB50EP
Pony express to mitochondria p468
Synthetic peptides that can enter the cell and localize to mitochondria are promising tools for delivering cargo to the organelle.
Irene Kaganman
doi:10.1038/nmeth0608-468
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwB60EQ
----------------------
NEWS AND VIEWS
----------------------
Super-resolution for a 3D world pp471 - 472
Technological developments are pushing the emerging super-resolution fluorescence microscopy techniques into the world of three-dimensional imaging.
Joshua W Shaevitz
doi:10.1038/nmeth0608-471
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwB70ER
Turning fluorescent proteins into energy-saving light bulbs pp472 - 473
Screening for photostability in addition to color and brightness creates better fluorescent proteins.
Gert-Jan Kremers and David W Piston
doi:10.1038/nmeth0608-472
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwB80ES
----------------------
REVIEWS
----------------------
Do-it-yourself guide: how to use the modern single-molecule toolkit pp475 - 489
Nils G Walter, Cheng-Yen Huang, Anthony J Manzo and Mohamed A Sobhy
doi:10.1038/nmeth.1215
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCA0Ec
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCB0Ed
Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy pp491 - 505
Keir C Neuman and Attila Nagy
doi:10.1038/nmeth.1218
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCC0Ee
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCD0Ef
A practical guide to single-molecule FRET pp507 - 516
Rahul Roy, Sungchul Hohng and Taekjip Ha
doi:10.1038/nmeth.1208
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCE0Eg
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCF0Eh
----------------------
PERSPECTIVE
----------------------
Laminar flow cells for single-molecule studies of DNA-protein interactions pp517 - 525
Laurence R Brewer and Piero R Bianco
doi:10.1038/nmeth.1217
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCG0Ei
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCH0Ej
----------------------
BRIEF COMMUNICATIONS
----------------------
Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples pp527 - 529
The ability to image thick volumes with invariant high axial and lateral resolution is a challenge for existing super-resolution fluorescence microscopy techniques. The combination of a double-plane detection scheme with fluorescence photoactivation microscopy (FPALM) allows three-dimensional sub-diffraction resolution imaging of samples as thick as whole cells.
Manuel F Juette et al.
doi:10.1038/nmeth.1211
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCI0Ek
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCJ0El
Femtosecond laser nanoaxotomy lab-on-a-chip for in vivo nerve regeneration studies pp531 - 533
Caenorhabditis elegans is an ideal model organism for studying nerve regrowth and functional recovery after in vivo axotomy, but its high mobility makes such experiments challenging. A microfluidic device capable of transient immobilization of individual worms for high-resolution imaging and laser-based nanoaxotomy is described.
Samuel X Guo et al.
doi:10.1038/nmeth.1203
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCK0Em
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCL0En
Next-generation high-density self-assembling functional protein arrays pp535 - 538
To date, the only way to array proteins with high density and high content has been to print purified proteins on a microarray surface. The next generation of nucleic acid programmable protein arrays (NAPPA) now allows thousands of proteins to be produced in situ on a microarray.
Niroshan Ramachandran et al.
doi:10.1038/nmeth.1210
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCM0Eo
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCN0Ep
=====================================================================
With our new LNA microRNA PCR system, your discovery starts
from 10 pg total RNA - you only need a single cell. You can
even detect high and low expressed microRNAs from the same sample,
as the dynamic range is 8 logs wide. Our PCR system combines
microRNA-specific primers and SYBR(R) Green detection.
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BmRG0En
=====================================================================
----------------------
ARTICLES
----------------------
Spherical nanosized focal spot unravels the interior of cells pp539 - 544
A fluorescence microscope relying entirely on focused light allows the generation of spherical focal fluorescence spots much smaller than the wavelength of light. This development, termed isoSTED, overcomes the resolution limitation imposed by the diffraction of light and permits three-dimensional nanoscale imaging inside cells with common fluorophores.
Roman Schmidt et al.
doi:10.1038/nmeth.1214
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCO0Eq
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCP0Er
Improving the photostability of bright monomeric orange and red fluorescent proteins pp545 - 551
Improved photostability of fluorescent proteins would benefit many applications but is usually an afterthought in selection screens. Setting photostability as the primary selection criterion in screens for improved fluorescent proteins yielded highly photostable variants of existing orange and red fluorescent proteins without compromising other beneficial characteristics.
Nathan C Shaner et al.
doi:10.1038/nmeth.1209
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCQ0Es
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCR0Et
Real-time imaging of the intracellular glutathione redox potential pp553 - 559
Analysis of intracellular redox-based processes is constrained by the limited choice of appropriate biosensors. Fusion of human glutaredoxin-1 to an existing redox-sensitive GFP results in a ratiometric biosensor that allows rapid and sensitive dynamic imaging of glutathione redox potential in living cells.
Marcus Gutscher et al.
doi:10.1038/nmeth.1212
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCS0Eu
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCT0Ev
Cell-surface protein-protein interaction analysis with time-resolved FRET and snap-tag technologies: application to GPCR oligomerization pp561 - 567
Many extracellular receptors are organized into complexes that may have functional implications. A combination of snap-tag protein labeling technology with time-resolved fluorescence resonance energy transfer (FRET) provides a method for the systematic analysis of higher-order protein-protein interactions on the surface of living cells.
Damien Maurel et al.
doi:10.1038/nmeth.1213
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCU0Ew
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCV0Ex
----------------------
TECHNOLOGY FEATURE
----------------------
Nanotechnology in biology: big collaborations for a small world pp569 - 574
In less than five years the Nano/Bio Interface Center at the University of Pennsylvania has gone from an idea to a nationally funded nanotechnology center. A look inside reveals how they have taken a collaborative approach to technology development.
Nathan Blow
doi:10.1038/nmeth0608-569
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCW0Ey
----------------------
ERRATA
----------------------
Erratum: Unexpected failure rates for modular assembly of engineered zinc fingers p575
Cherie L Ramirez et al.
doi:10.1038/nmeth0608-575a
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCX0Ez
Erratum: SNP genotyping: six technologies that keyed a revolution p575
Jeffrey Perkel
doi:10.1038/nmeth0608-575b
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCY0E1
----------------------
APPLICATION NOTES
----------------------
Liquidator 96 ready-to-use manual benchtop system
Jim Petrek and Murray Anderson
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCZ0E2
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCa0EA
Cellaxess[reg]HT: high-throughput transfection for genome-wide RNAi
Johan Pihl et al.
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCb0EB
Article: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80BwCc0EC
=====================================================================
Nature Reviews Stem Cell Collection
Free online access
Stem-cell research has a history of more than 20 years, and has made some outstanding contributions to our understanding of haematopoiesis and embryology. The Nature Reviews journals present a Stem Cell Collection, which includes Research Highlights, Reviews and Perspectives articles from Nature Reviews Cancer, Nature Reviews Immunology and Nature
Reviews Molecular Cell Biology.
All these articles will be available free online for six months at: http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80Bqfi0El
=====================================================================
You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at:
http://ealerts.nature.com/cgi-bin24/DM/y/elBs0Xztnp0Hi80Zzu0Eo
(You will need to log in to be recognised as a nature.com registrant).
For further technical assistance, please contact our registration department:
registration@nature.com
For print subscription enquiries, please contact our subscription department:
subscriptions@nature.com
For other enquiries, please contact our customer feedback department:
feedback@nature.com
Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA
Nature Publishing Group's worldwide offices:
London - Paris - Munich - New Delhi - Tokyo - Melbourne -
San Diego - San Francisco - Washington - New York - Boston
(c) Copyright 2008 Nature Publishing Group
=====================================================================
